I think you should keep doing what you are doing. My nethie had a lot of aggression problems before and after puberty. He has a lot of trust issues and his first thought is to attack. Were working on trust with him everyday and hes so much better than he used to be! Anyway, while hes relaxed on you, put your hand near him. Let him smell it, nudge it, sit on it, ect. After he gets comfortable around one hand, add in both hands. When hes comfortable with both hands around him, pet him. If he runs, dont try to pet him the next few times so he can get comfortable again. It might take a while but im sure he will learn to trust you. He may also just be territorial of his cage, in which you would want to take him out of his cage before putting your hands in there. If you can, get a towel or small fabric toy and sleep with it for a week or two, then put it in his cage. Itll get him used to your smell being in his territory

Rabbit language is a language of patience.
Mikey has a good advices there. You also might want to just sit nwxt to him. Do whatever you do and don’t pay attention on him, when he feels comfortable enough he will start checking you out. And from there on you can build.
From my experience it’s always good to leave them one spot at least where you won’t be mending so to say. No hends there when hi is in, or geting him out of there if he doesn’t want it (unless in a case of emergency of course)
They need to feel safe and at home. My Bianca was very scared when she came and it took her a while before she got relaxed but now she runs after me around the house just like Redford and even cuddle too.
As I said just patience, time and love. You are on a good way already!

Thats awesome! Glad you both are feeling much more comfortable with the few changes made. Sometimes thats all it takes